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- EMDB-9684: Cryo-EM structure of Echovirus 6 complexed with its attachment re... -

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Basic information

Entry
Database: EMDB / ID: EMD-9684
TitleCryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5
Map data
SampleCryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5:
(Capsid protein ...Capsid) x 4 / Complement decay-accelerating factor / ligand
Function / homology
Function and homology information


CD4-positive, alpha-beta T cell cytokine production / positive regulation of CD4-positive, alpha-beta T cell activation / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of complement-dependent cytotoxicity / ficolin-1-rich granule membrane / transport vesicle / anchored component of membrane ...CD4-positive, alpha-beta T cell cytokine production / positive regulation of CD4-positive, alpha-beta T cell activation / regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of complement-dependent cytotoxicity / ficolin-1-rich granule membrane / transport vesicle / anchored component of membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / complement activation, classical pathway / regulation of complement activation / virus receptor activity / positive regulation of cytosolic calcium ion concentration / endoplasmic reticulum to Golgi vesicle-mediated transport / lipid binding / Golgi membrane / membrane raft / innate immune response / neutrophil degranulation / cell surface / go:0005623: / extracellular exosome / extracellular region / plasma membrane
Sushi/SCR/CCP superfamily / Sushi/SCR/CCP domain
Complement decay-accelerating factor
Biological speciesEchovirus E6 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGao GF / Liu S / Zhao X / Peng R
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010000 China
CitationJournal: Cell / Year: 2019
Title: Human Neonatal Fc Receptor Is the Cellular Uncoating Receptor for Enterovirus B.
Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / ...Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / Yan Li / Meifan Zhang / Jianxun Qi / Han Wang / Ning Du / Yan Wu / Yuhai Bi / Shan Gao / Yi Shi / Jinghua Yan / Yong Zhang / Zhengde Xie / Wensheng Wei / George F Gao /
Abstract: Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for ...Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for coxsackievirus B in EV-B have been identified, receptors mediating virus entry, especially the uncoating process of echovirus and other EV-B remain obscure. Here, we found that human neonatal Fc receptor (FcRn) is the uncoating receptor for major EV-B. FcRn binds to the virus particles in the "canyon" through its FCGRT subunit. By obtaining multiple cryo-electron microscopy structures at different stages of virus entry at atomic or near-atomic resolution, we deciphered the underlying mechanisms of enterovirus attachment and uncoating. These structures revealed that different from the attachment receptor CD55, binding of FcRn to the virions induces efficient release of "pocket factor" under acidic conditions and initiates the conformational changes in viral particle, providing a structural basis for understanding the mechanisms of enterovirus entry.
Validation ReportPDB-ID: 6ilj

SummaryFull reportAbout validation report
History
DepositionOct 18, 2018-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.047
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.047
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ilj
  • Surface level: 0.047
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ilj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9684.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å
1.35 Å/pix.
x 400 pix.
= 540. Å
1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.047 / Movie #1: 0.047
Minimum - Maximum-0.16981389 - 0.2632968
Average (Standard dev.)0.0016313958 (±0.014584609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1700.2630.002

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Supplemental data

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Sample components

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Entire Cryo-EM structure of Echovirus 6 complexed with its attachment re...

EntireName: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5
Number of components: 7

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Component #1: protein, Cryo-EM structure of Echovirus 6 complexed with its atta...

ProteinName: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5
Recombinant expression: No
SourceSpecies: Echovirus E6

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Component #2: protein, Capsid protein VP1

ProteinName: Capsid protein VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.707332 kDa
SourceSpecies: Echovirus E6

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Component #3: protein, Capsid protein VP2

ProteinName: Capsid protein VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.06452 kDa
SourceSpecies: Echovirus E6

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Component #4: protein, Capsid protein VP3

ProteinName: Capsid protein VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.378936 kDa
SourceSpecies: Echovirus E6

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Component #5: protein, Capsid protein VP4

ProteinName: Capsid protein VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.338014 kDa
SourceSpecies: Echovirus E6

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Component #6: protein, Complement decay-accelerating factor

ProteinName: Complement decay-accelerating factor / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.307959 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: ligand, SPHINGOSINE

LigandName: SPHINGOSINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.299492 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 5.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 11494
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Output model

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